From d62311a643ae3ef42453ea1e30f4f5a429464593 Mon Sep 17 00:00:00 2001
From: juanf <juanf>
Date: Tue, 14 Apr 2015 15:12:11 +0000
Subject: [PATCH] SSDM-1728: YeastLab Data Curation - Report
SVN: 33831
---
.../stellingconsistency/consistency.py | 45 ++++++++++++++-----
1 file changed, 34 insertions(+), 11 deletions(-)
diff --git a/plasmid/source/core-plugins/stellingmigration/1/dss/drop-boxes/stellingconsistency/consistency.py b/plasmid/source/core-plugins/stellingmigration/1/dss/drop-boxes/stellingconsistency/consistency.py
index 2942d3fdcc6..2d0ea7e0051 100644
--- a/plasmid/source/core-plugins/stellingmigration/1/dss/drop-boxes/stellingconsistency/consistency.py
+++ b/plasmid/source/core-plugins/stellingmigration/1/dss/drop-boxes/stellingconsistency/consistency.py
@@ -9,22 +9,26 @@ import xml.etree.ElementTree as ET
##
sampleTypesToVerify = ["YEAST","POMBE"];
-logLevelsToPrint = ["ERROR", "REPORT", "MANUAL-FIX"];
+logLevelsToPrint = ["ERROR", "REPORT", "MANUAL-FIX", "AUTO-FIX-2"];
##
## Logging
##
numberOfManualFixes = 0;
-numberOfAutoFixes = 0;
+numberOfAutoFixesDeletes = 0;
+numberOfAutoFixesLost = 0;
def log(level, message):
if level == "MANUAL-FIX":
global numberOfManualFixes
numberOfManualFixes = numberOfManualFixes + 1
if level == "AUTO-FIX":
- global numberOfAutoFixes
- numberOfAutoFixes = numberOfAutoFixes + 1
- if any(level in s for s in logLevelsToPrint):
+ global numberOfAutoFixesDeletes
+ numberOfAutoFixesDeletes = numberOfAutoFixesDeletes + 1
+ if level == "AUTO-FIX-2":
+ global numberOfAutoFixesLost
+ numberOfAutoFixesLost = numberOfAutoFixesLost + 1
+ if level in logLevelsToPrint:
print "[" + level + "] " + message;
##
@@ -75,21 +79,23 @@ def process(tr):
verify(tr, sample)
global numberOfManualFixes
- global numberOfAutoFixes
- log("REPORT", "FOUND " + str(numberOfAutoFixes) + " AUTOMATIC FIXES!");
+ global numberOfAutoFixesDeletes
+ global numberOfAutoFixesLost
+ log("REPORT", "FOUND " + str(numberOfAutoFixesDeletes) + " AUTOMATIC DELETE FIXES!");
+ log("REPORT", "FOUND " + str(numberOfAutoFixesLost) + " AUTOMATIC LOST FIXES!");
log("REPORT", "REQUIRED " + str(numberOfManualFixes) + " MANUAL FIXES!");
log("REPORT", "FINISH VERIFICATION REPORT!");
def verify(tr, sample):
annotationsRoot = getAnnotationsRootNodeFromSample(sample)
- requiredAnnotationsFound = getRequiredAnnotations(sample)
- #1. Delete annotations and parent to be added
-
#1.Annotations hierarchy
+ requiredAnnotationsFound = getRequiredAnnotations(sample) #To detect case 4
+ requiredAnnotationsFromParents = getRequiredAnnotationsFromParents(sample) #To detect case 5
if annotationsRoot is not None:
for annotation in annotationsRoot:
annotatedSampleIdentifier = annotation.attrib["identifier"] #Identifier from annotated sample
requiredAnnotationsFound[annotatedSampleIdentifier] = True
+ requiredAnnotationsFromParents[annotatedSampleIdentifier] = True
try:
if isChild(sample, annotatedSampleIdentifier):
#This is an annotation from a parent, this is by default correct and don't needs further inspection.
@@ -110,10 +116,27 @@ def verify(tr, sample):
log("MANUAL-FIX", "CASE 2 - THE ANNOTATED SAMPLE IS NOT ANNOTATED WHERE IT SHOULD - FOR SAMPLE: " + sample.getSampleIdentifier() + " ANNOTATION: " + annotatedSampleIdentifier +" NOT AT " + foundAncestor.getSampleIdentifier());
except Exception, err:
log("ERROR", "PROCESSING ANNOTATIONS XML CHILD " + sample.getSampleIdentifier() + " ERR: " + str(err));
- #2.Missing Annotations
+ #2.Missing Parents Annotations
for parentIdentifier in requiredAnnotationsFound:
if not requiredAnnotationsFound[parentIdentifier]:
log("MANUAL-FIX", "CASE 4 - MISSING ANNOTATIONS ON SAMPLE: " + sample.getSampleIdentifier() + " FOR PARENT:" + parentIdentifier);
+ #3.Missing Annotations LOST
+ for parentAnnotationIdentifier in requiredAnnotationsFromParents:
+ if not requiredAnnotationsFromParents[parentAnnotationIdentifier]:
+ log("AUTO-FIX-2", "CASE 2 - MISSING LOST ANNOTATIONS ON SAMPLE: " + sample.getSampleIdentifier() + " FOR LOST:" + parentAnnotationIdentifier);
+
+def getRequiredAnnotationsFromParents(sample):
+ requiredAnnotationsFromParents = {}
+ for parentIdentifier in sample.getParentSampleIdentifiers():
+ if ("/FRY" in parentIdentifier) or ("/FRS" in parentIdentifier): #Only check Yeast and Pombe Parents
+ parent = getSampleFromCache(parentIdentifier)
+ parentAnnotationsRoot = getAnnotationsRootNodeFromSample(parent)
+ if parentAnnotationsRoot is not None:
+ for parentAnnotation in parentAnnotationsRoot:
+ parentAnnotationIdentifier = parentAnnotation.attrib["identifier"];
+ if "/FRP" in parentAnnotationIdentifier: #Only require Plasmids
+ requiredAnnotationsFromParents[parentAnnotationIdentifier] = False
+ return requiredAnnotationsFromParents;
def getRequiredAnnotations(sample):
requiredAnnotationsFound = {}
--
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